SNP ministers have accused of pervading over a culture of “evasiveness and secrecy” by blocking the publication of documents about their dealings with the Prince of Wales over Scottish education.

Holyrood’s opposition parties highlighted emails showing that John Swinney said he would “prefer” that material about Prince Charles be withheld from a Freedom of Information (FOI) response about Teach First, an education charity of which he is a patron.

They also disclosed that Colin McAllister, his senior political special adviser, was consulted and that civil servants “addressed” the points he made in their response.

The Tories, Labour and Lib Dems argued this contradicted assurances given by Joe Fitzpatrick, the Parliamentary Business Minister, that the replies were not screened by special advisers for political sensitivity and called for the Scottish Information Commissioner to investigate.

Although the Scottish Government published an FOI response in December showing that the prince privately lobbied Alex Salmond in 2013 about Teach First, it was not previously known that Mr Swinney had requested that some documents be kept secret.

Nicola Sturgeon defended her government’s record, saying it was “entirely appropriate” that opinions are sought from the “relevant parts” of her government, including over whether a response needs ministerial clearance.

But Mr Swinney, her deputy and the Education Minister, faced allegations in the Holyrood chamber of having been “caught ordering key documents to be withdrawn”.

Following a seven-month FOI battle with a journalist, the Scottish Government published an email dated June 30 last year regarding a previous request for correspondence about Teach First.

It said Mr Swinney would like officials to examine whether they “could not release the material relating to Prince Charles”, who is known as the Duke of Rothesay in Scotland, or his private secretary. The word ‘not’ was underlined.

The email said the Education Minister “specifically referenced documents 20, 24, 25, 26 as ones he’d prefer were not released.”

Another email showed officials telling Mr McAllister they had removed three documents under an FOI exemption covering “commercial interests” and asking him whether he was content for the draft response to be forwarded to Mr Swinney.

But when asked last June whether special advisers screened requests for politically damaging information, Mr Fitzpatrick responded: “No, requests are all prepared by Scottish Government officials. Special advisers have a role in assessing draft responses for accuracy.”

Sir Edward Mountain, a Tory MSP, said: “We now know that the answers given by Mr Fitzpatrick to the Scottish Parliament are not true.

“The evidence suggests that special advisers are routinely involved in the freedom of information process for political purposes and John Swinney himself is suppressing documents when it suits him.”

Tavish Scott, a Lib Dem MSP, said he had written to the information commissioner asking him to investigate. He added: “Sadly what we have seen this week is more evidence of the culture of evasiveness and secrecy that guides the Scottish Government’s approach to open information.”

A letter from the commissioner to Mr Fitzpatrick was published setting out the questions he intends to investigate, including the role of special advisers “in the request handling process” and whether this was to the “detriment” of information being released.

But Ms Sturgeon told MSPs: “At all times, freedom of information requests are handled in line with the legislation, including consideration of whether particular exemptions are applied.”

A Scottish Government spokesman said: “The legal duty to comply with FOI legislation lies with Scottish ministers. As ministers are accountable it is entirely appropriate for them to decide whether they are content with proposed information releases and exemptions applied in line with the FOI Act.”